There are no static filters, so it's highly unlikely that spam/junk filtering is slowing things down. Thunderbird uses an adaptive filter that learns from your actions which messages are legitimate and which are junk. https://support.mozilla.org/en-US/kb/thunderbird-and-junk-spam-messages

I 'm not sure you are correct. Over the last few months one of my accounts has been receiving a lot of spam/scam emails in the inbox, 20 to 50 a day. I have been identifying them by clicking on the spam status icon. These then automatically move to the junk folder and future ones are also moved, however, there are still many coming in every day. I am in the process of eliminating the use of this email address but since it has been my go to address since e-mailing became available you can imagine how many sites it has been used on. In the mean time I want to reduce the number I have to handle.

I am sitting here watching Thunderbird work through my inbox and it is now taking up to 5 seconds to identify and move the spam to the junk box. This says to me that it is using some kind of reference file to identify these messages because it seems like some messages are further down the list than others. What I am hoping to do is to somehow fix this reference to target them more generally to reduce duplication in the reference.

Are you accumulating messages in Inbox?

What is the size of your Inbox folder on disk?

What is your anti-virus software?

Right now there about 1200 but am in the process of cleaning that up. Any messages I need to save are moved to folders in the Local Folders area.

Inbox folder is 27kb

I use AOS's (Advanced System Optimizer) System Protector.

Inbox folder is 27kb

Well, that shouldn't cause problems.

As a test, try to start Windows 10 in safe mode with networking enabled.

Does the problem go away?

Windows safe mode disables anti-virus software. This is a troubleshooting step, not a solution.